DNA preparation and purification is essential to virtually all molecular biology. Most methods now in use for purifying double-stranded DNA from bacterial lysates rely on labor-intensive organic extractions and/or centrifugation. These techniques are not readily automated. Yet, as large-scale molecular biology projects such as the Human Genome Initiative move forward, automation of every phase of DNA analysis will become increasingly important.
In recent years, a new class of analytical and purification techniques have been developed which rely upon inherent biological affinities between proteins, between enzymes and their substrates, and between proteins and nucleic acids. Some affinity techniques exploit the exquisite specificity of monoclonal or polyclonal antibodies for particular counterpart antigens and haptens. In other techniques, target molecules are tagged with small molecules which are themselves the affinity target for other, more readily detectable or tangible molecules.
Affinity techniques are attractive because the desired molecules are rapidly and specifically immobilized away from the other contaminating molecules in an impure mixture, offering rapid and extensive purification or enrichment levels unachievable using classic techniques. Contaminating molecules are simply washed away, while target molecules remain firmly affinity-bound. Target molecules may be detached from their counterpart molecules simply by altering the environment to disfavor the affinity between the two. A second advantage of affinity purification techniques is that immobilization, detachment, and elution of target molecules are all relatively straightforward to automate.
Assays for particular DNA sequences are also performed based on DNA-DNA interactions. Typically, however, such interactions are based on the hybridization of a single-stranded DNA probe to a single stranded target DNA sequence. Hence, in a sample from a biological source, the normally double-stranded DNA must be denatured into a single-stranded state for the assay. This need for denaturing makes this hybridization technique unsuited for capture of double-stranded DNA.
What is lacking in the art is the ability to affinity-capture double-stranded DNA molecules using an immobilized nucleic acid. Since nucleic acids are easily synthesized, cloned, sequenced, and modified as desired, a nucleic acid affinity capture procedure is desirable.